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Journal Article

Whole-brain functional ultrasound imaging in awake head-fixed mice


Macé,  Emilie
Max Planck Research Group: Brain-Wide Circuits for Behavior / Macé, MPI of Neurobiology, Max Planck Society;

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Brunner, C., Grillet, M., Urban, A., Roska, B., Montaldo, G., & Macé, E. (2021). Whole-brain functional ultrasound imaging in awake head-fixed mice. Nature Protocols, 16(7), 3547-3571. doi:10.1038/s41596-021-00548-8.

Cite as: https://hdl.handle.net/21.11116/0000-0009-9C9C-8
Most brain functions engage a network of distributed regions. Full
investigation of these functions thus requires assessment of whole
brains; however, whole-brain functional imaging of behaving animals
remains challenging. This protocol describes how to follow brain-wide
activity in awake head-fixed mice using functional ultrasound imaging, a
method that tracks cerebral blood volume dynamics. We describe how to
set up a functional ultrasound imaging system with a provided
acquisition software (miniScan), establish a chronic cranial window
(timing surgery: similar to 3-4 h) and image brain-wide activity
associated with a stimulus at high resolution (100 x 110 x 300 mu m and
10 Hz per brain slice, which takes similar to 45 min per imaging
session). We include codes that enable data to be registered to a
reference atlas, production of 3D activity maps, extraction of the
activity traces of similar to 250 brain regions and, finally,
combination of data from multiple sessions (timing analysis averages
similar to 2 h). This protocol enables neuroscientists to observe global
brain processes in mice.